Contacts of the helix formed by residues 350 - 369 (chain B) in PDB entry 4D2Y
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with THR 350 (chain B).
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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349B ARG* 1.3 78.7 - - - +
351B LYS* 1.3 65.6 + - - +
352B ASP* 3.0 18.8 + - - +
353B GLN* 3.0 34.5 + - - +
354B LEU* 3.1 22.0 + - - +
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Residues in contact with LYS 351 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ARG 4.0 1.6 + - - -
350B THR* 1.3 72.5 - - - +
352B ASP* 1.3 67.9 + - + +
354B LEU* 3.4 15.4 + - - +
355B PHE* 3.6 11.4 + - - +
388B ILE* 3.3 37.1 + - + +
389B GLU* 3.5 23.8 + - + +
392B SER* 3.3 33.5 + - - +
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Residues in contact with ASP 352 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
350B THR* 3.2 20.6 - - - +
351B LYS* 1.3 83.7 - - - +
353B GLN* 1.3 67.4 + - - +
355B PHE* 5.2 0.2 - - - +
356B PRO* 3.6 14.0 - - - +
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Residues in contact with GLN 353 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ARG* 3.8 27.0 - - + +
350B THR* 3.0 42.0 + - - +
352B ASP* 1.3 86.7 + - - +
354B LEU* 1.3 62.8 + - - +
355B PHE 3.6 0.2 - - - -
356B PRO* 3.2 20.0 - - + +
357B LEU* 3.4 20.4 - - + +
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Residues in contact with LEU 354 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
349B ARG* 4.6 14.4 - - + +
350B THR 3.1 14.3 + - - +
351B LYS* 3.9 7.9 - - - +
352B ASP 3.3 1.2 - - - -
353B GLN* 1.3 80.1 - - + +
355B PHE* 1.3 59.4 + - - +
357B LEU* 3.1 6.6 + - - +
358B ALA* 2.8 25.8 + - - +
388B ILE* 4.1 17.5 - - + -
392B SER 3.7 23.3 - - - +
393B THR* 3.9 17.9 - - - +
394B TYR* 4.4 8.1 - - + -
575B GLY 3.9 5.2 - - - +
576B GLY* 3.6 39.0 - - - +
577B LEU* 4.6 3.6 - - + -
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Residues in contact with PHE 355 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
351B LYS 3.6 9.7 + - - +
352B ASP 5.2 0.2 - - - +
354B LEU* 1.3 77.7 - - - +
356B PRO* 1.4 66.6 - - + +
358B ALA* 3.1 2.9 + - + +
359B LYS* 2.7 53.7 + - + +
362B LEU* 6.0 0.2 - - + -
381B LEU* 3.6 28.9 - - + -
384B VAL* 4.2 7.9 - - + -
385B ASN* 3.3 52.5 - - + +
388B ILE* 3.8 22.1 - - + +
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Residues in contact with PRO 356 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
352B ASP 3.6 14.8 - - - +
353B GLN* 3.2 22.9 - - - +
355B PHE* 1.4 96.1 - - + +
357B LEU* 1.3 57.2 + - + +
359B LYS* 3.7 8.7 - - + +
360B GLU* 2.9 30.8 + - - +
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Residues in contact with LEU 357 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
321B THR* 6.0 1.8 - - + +
349B ARG* 3.7 40.2 - - - +
353B GLN* 3.4 20.4 - - + +
354B LEU* 3.1 8.8 + - - +
356B PRO* 1.3 76.2 - - + +
358B ALA* 1.3 65.7 + - - +
360B GLU* 3.6 19.3 + - - +
361B PHE* 3.2 16.6 + - - +
573B GLU* 4.4 8.3 - - - +
575B GLY* 3.6 12.1 - - - -
576B GLY* 3.9 20.6 - - - +
701B THR* 6.0 2.9 - - + +
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Residues in contact with ALA 358 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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354B LEU 2.8 13.3 + - - +
355B PHE* 3.5 9.0 - - + +
357B LEU* 1.3 77.4 - - - +
359B LYS* 1.3 57.9 + - - +
361B PHE* 3.2 3.5 + - - +
362B LEU* 2.8 35.1 + - + +
384B VAL* 3.8 21.8 - - + -
388B ILE* 4.2 3.6 - - + -
394B TYR* 3.7 29.4 - - + +
575B GLY* 3.6 8.4 + - - -
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Residues in contact with LYS 359 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
355B PHE* 2.7 42.2 + - + +
356B PRO* 3.7 7.9 - - + +
358B ALA* 1.3 75.0 - - - +
360B GLU* 1.3 57.7 + - - +
362B LEU* 3.7 0.9 - - - +
363B ASP* 2.8 65.5 + - - +
372B PHE* 6.2 0.4 - - - -
381B LEU* 4.2 30.2 - - + +
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Residues in contact with GLU 360 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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319B LYS 4.4 5.7 - - - +
321B THR* 3.6 26.0 - - - +
356B PRO 2.9 17.2 + - - +
357B LEU* 3.9 23.8 - - - +
359B LYS* 1.3 76.4 - - - +
361B PHE* 1.3 62.8 + - - +
363B ASP* 3.3 8.5 + - - +
364B GLN* 3.0 38.0 + - + +
701B THR* 4.0 18.7 + - - -
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Residues in contact with PHE 361 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
357B LEU 3.2 3.1 + - - +
358B ALA 3.2 5.2 + - - +
360B GLU* 1.3 81.8 - - - +
362B LEU* 1.3 67.9 + - + +
364B GLN* 3.0 14.0 + - - +
365B TYR* 2.8 28.5 + - + +
394B TYR* 4.6 1.1 - - - -
396B LEU* 3.7 26.5 - - + -
400B GLU* 3.5 32.3 - - + -
403B TYR* 3.6 31.2 - + - -
404B GLY* 4.0 0.9 - - - -
574B ILE* 3.4 22.4 - - + -
575B GLY* 3.5 32.1 - - - +
702B PRO* 3.8 23.3 - - + -
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Residues in contact with LEU 362 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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355B PHE* 6.0 0.4 - - + -
358B ALA* 2.8 23.5 + - + +
359B LYS 4.0 0.2 - - - +
361B PHE* 1.3 79.6 - - + +
363B ASP* 1.3 60.5 + - - +
365B TYR* 4.2 3.1 - - + -
366B TYR* 2.9 45.9 + - + +
377B HIS* 3.9 2.7 - - + +
380B ARG* 3.8 15.0 - - + +
381B LEU* 3.7 30.3 - - + -
384B VAL* 3.6 35.9 - - + -
394B TYR* 5.4 3.1 - - + +
396B LEU* 5.6 1.3 - - + -
400B GLU* 3.4 37.0 - - + +
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Residues in contact with ASP 363 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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359B LYS* 2.8 53.2 + - - +
360B GLU* 3.4 8.3 - - - +
361B PHE 3.2 0.2 - - - -
362B LEU* 1.3 77.6 - - - +
364B GLN* 1.3 61.0 + - - +
367B SER* 2.9 30.7 + - - -
372B PHE* 3.7 23.1 - - + -
377B HIS* 3.0 25.7 + - - -
381B LEU* 4.2 3.8 - - - +
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Residues in contact with GLN 364 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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360B GLU* 3.0 37.1 + - + +
361B PHE* 3.0 15.1 + - - +
363B ASP* 1.3 75.4 - - + +
365B TYR* 1.3 64.7 + - - +
367B SER* 3.3 6.6 + - - -
368B SER* 3.0 19.8 + - - -
403B TYR* 3.6 26.8 + - + +
407B HIS* 5.3 2.3 + - - -
411B ASN* 5.6 0.2 + - - -
669B ARG* 5.6 3.3 + - - -
701B THR* 3.3 32.7 + - - +
702B PRO* 3.7 11.9 - - - +
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Residues in contact with TYR 365 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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361B PHE* 2.8 25.3 + - + +
362B LEU* 3.8 6.7 - - + +
364B GLN* 1.3 73.9 - - - +
366B TYR* 1.3 91.8 + + - +
368B SER* 2.7 22.4 + - - -
369B ILE* 3.2 45.2 + - + +
399B THR* 3.2 44.3 + - - +
400B GLU* 3.9 20.0 - - + -
403B TYR* 3.7 37.2 - + + -
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Residues in contact with TYR 366 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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362B LEU* 2.9 31.7 + - + +
365B TYR* 1.3 96.8 - + - +
367B SER* 1.3 63.2 + - - +
369B ILE* 3.4 23.5 + - + +
370B LYS 3.3 3.3 + - - -
371B ARG* 2.8 41.9 + - + +
372B PHE* 3.9 2.7 - - - -
376B ALA* 3.5 19.9 + - + +
377B HIS* 3.5 54.3 - + + +
380B ARG* 3.4 36.8 - - + +
400B GLU* 4.4 3.4 + - - -
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Residues in contact with SER 367 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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363B ASP 2.9 23.0 + - - -
364B GLN* 3.6 6.5 - - - -
365B TYR 3.3 0.2 - - - -
366B TYR* 1.3 75.7 - - - +
368B SER* 1.3 57.6 + - - +
370B LYS* 2.9 29.8 + - - +
372B PHE* 3.2 27.5 - - - +
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Residues in contact with SER 368 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
----------------------------------------------------------
364B GLN 3.0 9.6 + - - -
365B TYR* 2.7 18.0 + - - -
367B SER* 1.3 76.7 - - - +
369B ILE* 1.3 64.3 + - - +
370B LYS* 3.5 7.3 + - - +
403B TYR* 3.2 36.8 - - - -
407B HIS* 5.3 2.7 - - - -
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Residues in contact with ILE 369 (chain B).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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365B TYR* 3.2 52.9 + - + +
366B TYR* 3.4 31.4 - - + +
367B SER 3.2 0.2 - - - -
368B SER* 1.3 83.1 + - - +
370B LYS* 1.3 68.6 + - - +
371B ARG* 3.2 28.1 + - + +
403B TYR* 6.0 0.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
------------------------------------------------------------
I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il